Observation data class for IODA. More...

#include <ObsSpace.h>

Inheritance diagram for ioda::ObsSpace:

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Public Types
typedef std::map< std::size_t, std::vector< std::size_t > >	RecIdxMap

typedef RecIdxMap::const_iterator	RecIdxIter

typedef ObsTopLevelParameters	Parameters_

Public Member Functions
	ObsSpace (const Parameters_ &params, const eckit::mpi::Comm &comm, const util::DateTime &bgn, const util::DateTime &end, const eckit::mpi::Comm &timeComm)
	Config based constructor for an ObsSpace object. More...

	ObsSpace (const ObsSpace &)

virtual	~ObsSpace ()

const util::DateTime &	windowStart () const

const util::DateTime &	windowEnd () const

const eckit::mpi::Comm &	comm () const

const ObsSpaceParameters &	params () const

void	save ()
	save the obs space data into a file (if obsdataout specified) More...

std::size_t	globalNumLocs () const
	return the total number of locations in the corresponding obs spaces across all MPI tasks More...

std::size_t	globalNumLocsOutsideTimeWindow () const
	return number of locations from obs source that were outside the time window More...

size_t	nlocs () const
	return the number of locations in the obs space. Note that nlocs may be smaller than global unique nlocs due to distribution of obs across multiple process elements. More...

size_t	nchans () const
	return the number of channels in the container. If this is not a radiance obs type, then this will return zero. More...

std::size_t	nrecs () const
	return the number of records in the obs space container More...

std::size_t	nvars () const
	return the number of variables in the obs space container. "Variables" refers to the quantities that can be assimilated as opposed to meta data. More...

std::string	get_dim_name (const ObsDimensionId dimId) const
	return the standard dimension name for the given dimension id More...

std::size_t	get_dim_size (const ObsDimensionId dimId) const
	return the standard dimension size for the given dimension id More...

ObsDimensionId	get_dim_id (const std::string &dimName) const
	return the standard dimension id for the given dimension name More...

const std::vector< std::string > &	obs_group_vars () const
	return YAML configuration parameter: obsdatain.obsgrouping.group variables More...

std::string	obs_sort_var () const
	return YAML configuration parameter: obsdatain.obsgrouping.sort variable More...

std::string	obs_sort_order () const
	return YAML configuration parameter: obsdatain.obsgrouping.sort order More...

const std::string &	obsname () const
	return the name of the obs type being stored More...

std::string	distname () const
	return the name of the MPI distribution More...

const std::vector< std::size_t > &	recnum () const
	return reference to the record number vector More...

const std::vector< std::size_t > &	index () const
	return reference to the index vector More...

bool	has (const std::string &group, const std::string &name, bool skipDerived=false) const
	return true if variable `name` exists in group `group` or (unless `skipDerived` is set to true) `"Derived" +`group`. More...

ObsDtype	dtype (const std::string &group, const std::string &name, bool skipDerived=false) const
	return data type for group/variable More...

void	get_db (const std::string &group, const std::string &name, std::vector< int > &vdata, const std::vector< int > &chanSelect={ }, bool skipDerived=false) const
	transfer data from the obs container to vdata More...

void	get_db (const std::string &group, const std::string &name, std::vector< float > &vdata, const std::vector< int > &chanSelect={ }, bool skipDerived=false) const

void	get_db (const std::string &group, const std::string &name, std::vector< double > &vdata, const std::vector< int > &chanSelect={ }, bool skipDerived=false) const

void	get_db (const std::string &group, const std::string &name, std::vector< std::string > &vdata, const std::vector< int > &chanSelect={ }, bool skipDerived=false) const

void	get_db (const std::string &group, const std::string &name, std::vector< util::DateTime > &vdata, const std::vector< int > &chanSelect={ }, bool skipDerived=false) const

void	put_db (const std::string &group, const std::string &name, const std::vector< int > &vdata, const std::vector< std::string > &dimList={ "nlocs" })
	transfer data from vdata to the obs container More...

void	put_db (const std::string &group, const std::string &name, const std::vector< float > &vdata, const std::vector< std::string > &dimList={ "nlocs" })

void	put_db (const std::string &group, const std::string &name, const std::vector< double > &vdata, const std::vector< std::string > &dimList={ "nlocs" })

void	put_db (const std::string &group, const std::string &name, const std::vector< std::string > &vdata, const std::vector< std::string > &dimList={ "nlocs" })

void	put_db (const std::string &group, const std::string &name, const std::vector< util::DateTime > &vdata, const std::vector< std::string > &dimList={ "nlocs" })

const RecIdxIter	recidx_begin () const
	Return the begin iterator associated with the recidx_ data member. More...

const RecIdxIter	recidx_end () const
	Return the end iterator associated with the recidx_ data member. More...

bool	recidx_has (const std::size_t recNum) const
	true if given record number exists in the recidx_ data member More...

bool	obsAreSorted () const
	true if the groups in the recidx data member are sorted More...

std::size_t	recidx_recnum (const RecIdxIter &irec) const
	return record number pointed to by the given iterator More...

const std::vector< std::size_t > &	recidx_vector (const RecIdxIter &irec) const
	return record number vector pointed to by the given iterator More...

const std::vector< std::size_t > &	recidx_vector (const std::size_t recNum) const
	return record number vector selected by the given record number More...

std::vector< std::size_t >	recidx_all_recnums () const
	return all record numbers from the recidx_ data member More...

const oops::Variables &	obsvariables () const
	return the collection of all simulated variables More...

const oops::Variables &	initial_obsvariables () const
	return the collection of simulated variables loaded from the input file More...

const oops::Variables &	derived_obsvariables () const
	return the collection of derived simulated variables (variables computed after loading the input file) More...

std::shared_ptr< const Distribution >	distribution () const
	return MPI distribution object More...

template<typename VarType >
bool	readObsSource (ObsFrameRead &obsFrame, const std::string &varName, std::vector< VarType > &varValues)

template<>
bool	readObsSource (ObsFrameRead &obsFrame, const std::string &varName, std::vector< std::string > &varValues)

template<typename VarType >
void	loadVar (const std::string &group, const std::string &name, const std::vector< int > &chanSelect, std::vector< VarType > &varValues, bool skipDerived) const

template<typename VarType >
void	saveVar (const std::string &group, std::string name, const std::vector< VarType > &varValues, const std::vector< std::string > &dimList)

template<typename VarType >
void	storeVar (const std::string &varName, std::vector< VarType > &varValues, const Dimensions_t frameStart, const Dimensions_t frameCount)

template<typename DataType >
void	extendVariable (Variable &extendVar, const size_t upperBoundOnGlobalNumOriginalRecs)

Private Member Functions
ObsSpace &	operator= (const ObsSpace &)=delete
	disable the "=" operator More...

void	print (std::ostream &os) const
	print function for oops::Printable class More...

void	createObsGroupFromObsFrame (ObsFrameRead &obsFrame)
	Initialize the database from a source (ObsFrame ojbect) More...

void	extendObsSpace (const ObsExtendParameters &params)
	Extend the ObsSpace according to the method requested in the configuration file. More...

void	createMissingObsErrors ()
	For each simulated variable that doesn't have an accompanying array in the ObsError or DerivedObsError group, create one, fill it with missing values and add it to the DerivedObsError group. More...

void	saveToFile ()
	Dump the database into the output file. More...

void	buildSortedObsGroups ()
	Create the recidx data structure holding sorted record groups. More...

void	buildRecIdxUnsorted ()
	Create the recidx data structure with unsorted record groups. More...

void	initFromObsSource (ObsFrameRead &obsFrame)
	initialize the in-memory obs_group_ (ObsGroup) object from the ObsIo source More...

void	resizeNlocs (const Dimensions_t nlocsSize, const bool append)
	resize along nlocs dimension More...

template<typename VarType >
bool	readObsSource (ObsFrameRead &obsFrame, const std::string &varName, std::vector< VarType > &varValues)
	read in values for variable from obs source More...

template<typename VarType >
void	storeVar (const std::string &varName, std::vector< VarType > &varValues, const Dimensions_t frameStart, const Dimensions_t frameCount)
	store a variable in the obs_group_ object More...

template<typename DataType >
DataType	getFillValue ()
	get fill value for use in the obs_group_ object More...

template<typename VarType >
void	loadVar (const std::string &group, const std::string &name, const std::vector< int > &chanSelect, std::vector< VarType > &varValues, bool skipDerived=false) const
	load a variable from the obs_group_ object More...

template<typename VarType >
void	saveVar (const std::string &group, std::string name, const std::vector< VarType > &varValues, const std::vector< std::string > &dimList)
	save a variable to the obs_group_ object More...

std::size_t	createChannelSelections (const Variable &variable, std::size_t nchansDimIndex, const std::vector< int > &channels, Selection &memSelect, Selection &obsGroupSelect) const
	Create selections of slices of the variable `variable` along dimension `nchansDimIndex` corresponding to channels `channels`. More...

void	createVariables (const Has_Variables &srcVarContainer, Has_Variables &destVarContainer, const VarDimMap &dimsAttachedToVars)
	create set of variables from source variables and lists More...

template<typename VarType >
Variable	openCreateVar (const std::string &varName, const std::vector< std::string > &varDimList)
	open an obs_group_ variable, create the varialbe if necessary More...

void	fillChanNumToIndexMap ()
	fill in the channel number to channel index map More...

void	splitChanSuffix (const std::string &group, const std::string &name, const std::vector< int > &chanSelect, std::string &nameToUse, std::vector< int > &chanSelectToUse, bool skipDerived=false) const
	split off the channel number suffix from a given variable name More...

template<typename DataType >
void	extendVariable (Variable &extendVar, const size_t upperBoundOnGlobalNumOriginalRecs)
	Extend the given variable. More...

Private Attributes
const util::DateTime	winbgn_
	Beginning of DA timing window. More...

const util::DateTime	winend_
	End of DA timing window. More...

const eckit::mpi::Comm &	commMPI_
	MPI communicator. More...

std::size_t	gnlocs_
	total number of locations More...

std::size_t	gnlocs_outside_timewindow_
	number of nlocs from the obs source that are outside the time window More...

std::size_t	nrecs_
	number of records More...

ObsDimInfo	dim_info_
	dimension information for variables in this obs space More...

std::map< int, int >	chan_num_to_index_
	map to go from channel number (not necessarily consecutive) to channel index (consecutive, starting from zero). More...

ObsGroup	obs_group_
	observation data store More...

ObsSpaceParameters	obs_params_
	obs io parameters More...

std::string	obsname_
	name of obs space More...

oops::Variables	obsvars_
	Observation "variables" to be simulated. More...

std::shared_ptr< const Distribution >	dist_
	MPI distribution object. More...

std::vector< std::size_t >	indx_
	indexes of locations to extract from the input obs file More...

std::vector< std::size_t >	recnums_
	record numbers associated with the location indexes More...

RecIdxMap	recidx_
	profile ordering More...

bool	recidx_is_sorted_
	indicator whether the data in recidx_ is sorted More...

VarDimMap	dims_attached_to_vars_
	map showing association of dim names with each variable name More...

std::map< std::vector< std::string >, Selection >	known_fe_selections_
	cache for frontend selection More...

std::map< std::vector< std::string >, Selection >	known_be_selections_
	cache for backend selection More...

Detailed Description

Observation data class for IODA.

This class handles the memory store of observation data. It handles the transfer of data between memory and files, the distribution of obs data across multiple process elements, the filtering out of obs data that is outside the DA timing window, the transfer of data between UFO, OOPS and IODA, and data type conversion that is "missing value aware".

During the DA run, all data transfers are done in memory. The only time file I/O is invoked is during the constructor (read from the file into the obs container) and optionally during the the destructor (write from obs container into the file).

Definition at line 116 of file src/ObsSpace.h.

Member Typedef Documentation

◆ Parameters_

typedef ObsTopLevelParameters ioda::ObsSpace::Parameters_

Definition at line 121 of file src/ObsSpace.h.

◆ RecIdxIter

typedef RecIdxMap::const_iterator ioda::ObsSpace::RecIdxIter

Definition at line 120 of file src/ObsSpace.h.

◆ RecIdxMap

typedef std::map<std::size_t, std::vector<std::size_t> > ioda::ObsSpace::RecIdxMap

Definition at line 119 of file src/ObsSpace.h.

Constructor & Destructor Documentation

◆ ObsSpace() [1/2]

ioda.ioda.ObsSpace::ObsSpace	(	const Parameters_ &	params,
		const eckit::mpi::Comm &	comm,
		const util::DateTime &	bgn,
		const util::DateTime &	end,
		const eckit::mpi::Comm &	timeComm
	)

Config based constructor for an ObsSpace object.

This constructor will read in from the obs file and transfer the variables into the obs container. Obs falling outside the DA timing window, specified by bgn and end, will be discarded before storing them in the obs container.

Parameters

params	Configuration parameters (an instance of ObsTopLevelParameters)
comm	MPI communicator for model grouping
bgn	DateTime object holding the start of the DA timing window
end	DateTime object holding the end of the DA timing window
timeComm	MPI communicator for ensemble

Config based constructor for an ObsSpace object. This constructor will read in from the obs file and transfer the variables into the obs container. Obs falling outside the DA timing window, specified by bgn and end, will be discarded before storing them in the obs container.

Parameters

[in]	config	ECKIT configuration segment holding obs types specs
[in]	comm	MPI communicator containing all processes that hold the observations for a given time slot or sub-window.
[in]	bgn	DateTime object holding the start of the DA timing window
[in]	end	DateTime object holding the end of the DA timing window
[in]	time	MPI communicator across time so that the 2D array of processes represented by the product of the comm and time communicators hold all observations in the ObsSpace.

If save_obs_distribution set to true, global location indices and record numbers will be stored in the MetaData/saved_index and MetaData/saved_record_number variables, respectively. These variables will be saved along with all other variables to the output files generated if the obsdataout.obsfile option is set.

When the "obsdatain.read obs from separate file" option is set for later runs, each process reads a separate input file directly, the presence of these variables makes it possible to identify observations stored in more than one input file.

Definition at line 112 of file ObsSpace.cc.

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◆ ObsSpace() [2/2]

ioda::ObsSpace::ObsSpace ( const ObsSpace & )

◆ ~ObsSpace()

virtual ioda::ObsSpace::~ObsSpace ( )

inlinevirtual

Definition at line 140 of file src/ObsSpace.h.

Member Function Documentation

◆ buildRecIdxUnsorted()

void ioda::ObsSpace::buildRecIdxUnsorted ( )

private

Create the recidx data structure with unsorted record groups.

This method will initialize the recidx structure without any particular ordering of the record groups.

Definition at line 1058 of file ObsSpace.cc.

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◆ buildSortedObsGroups()

void ioda::ObsSpace::buildSortedObsGroups ( )

private

Create the recidx data structure holding sorted record groups.

This method will construct a data structure that holds the location order within each group sorted by the values of the specified sort variable.

Definition at line 1009 of file ObsSpace.cc.

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◆ comm()

const eckit::mpi::Comm& ioda::ObsSpace::comm ( ) const

inline

This method will return the associated MPI communicator

Definition at line 149 of file src/ObsSpace.h.

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◆ createChannelSelections()

std::size_t ioda::ObsSpace::createChannelSelections	(	const Variable &	variable,
		std::size_t	nchansDimIndex,
		const std::vector< int > &	channels,
		Selection &	memSelect,
		Selection &	obsGroupSelect
	)		const

private

Create selections of slices of the variable variable along dimension nchansDimIndex corresponding to channels channels.

Returns: The number of elements in each selection.

Definition at line 808 of file ObsSpace.cc.

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◆ createMissingObsErrors()

void ioda::ObsSpace::createMissingObsErrors ( )

private

For each simulated variable that doesn't have an accompanying array in the ObsError or DerivedObsError group, create one, fill it with missing values and add it to the DerivedObsError group.

Definition at line 1316 of file ObsSpace.cc.

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◆ createObsGroupFromObsFrame()

void ioda::ObsSpace::createObsGroupFromObsFrame ( ObsFrameRead & obsFrame )

private

Initialize the database from a source (ObsFrame ojbect)

Parameters

obsFrame obs source object

Definition at line 446 of file ObsSpace.cc.

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◆ createVariables()

void ioda::ObsSpace::createVariables	(	const Has_Variables &	srcVarContainer,
		Has_Variables &	destVarContainer,
		const VarDimMap &	dimsAttachedToVars
	)

private

create set of variables from source variables and lists

Parameters

srcVarContainer	Has_Variables object from source
destVarContainer	Has_Variables object from destination
dimsAttachedToVars	Map containing list of attached dims for each variable

Definition at line 923 of file ObsSpace.cc.

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◆ derived_obsvariables()

const oops::Variables& ioda::ObsSpace::derived_obsvariables ( ) const

inline

return the collection of derived simulated variables (variables computed after loading the input file)

Definition at line 357 of file src/ObsSpace.h.

◆ distname()

std::string ioda::ObsSpace::distname ( ) const

inline

return the name of the MPI distribution

Definition at line 220 of file src/ObsSpace.h.

◆ distribution()

std::shared_ptr<const Distribution> ioda::ObsSpace::distribution ( ) const

inline

return MPI distribution object

Definition at line 361 of file src/ObsSpace.h.

◆ dtype()

ObsDtype ioda::ObsSpace::dtype	(	const std::string &	group,
		const std::string &	name,
		bool	skipDerived = `false`
	)		const

return data type for group/variable

Parameters

group	Group name containting the variable
name	Variable name
skipDerived	By default, this function will look for the variable `name` in the group `"Derived" + group` first and only if it doesn't exist will it look in the group `group`. Set this parameter to `true` to look only in the group `group`.

Definition at line 274 of file ObsSpace.cc.

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◆ extendObsSpace()

void ioda::ObsSpace::extendObsSpace ( const ObsExtendParameters & params )

private

Extend the ObsSpace according to the method requested in the configuration file.

Parameters

params object containing specs for extending the ObsSpace

Definition at line 1182 of file ObsSpace.cc.

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◆ extendVariable() [1/2]

template<typename DataType >

void ioda::ObsSpace::extendVariable	(	Variable &	extendVar,
		const size_t	upperBoundOnGlobalNumOriginalRecs
	)

Definition at line 1145 of file ObsSpace.cc.

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◆ extendVariable() [2/2]

template<typename DataType >

void ioda::ObsSpace::extendVariable	(	Variable &	extendVar,
		const size_t	upperBoundOnGlobalNumOriginalRecs
	)

private

Extend the given variable.

Parameters

extendVar	database variable to be extended
upperBoundOnGlobalNumOriginalRecs	upper bound, across all processors, of the number of records in the original ObsSpace.

◆ fillChanNumToIndexMap()

void ioda::ObsSpace::fillChanNumToIndexMap ( )

private

fill in the channel number to channel index map

Definition at line 966 of file ObsSpace.cc.

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◆ get_db() [1/5]

void ioda::ObsSpace::get_db	(	const std::string &	group,
		const std::string &	name,
		std::vector< double > &	vdata,
		const std::vector< int > &	chanSelect = `{ }`,
		bool	skipDerived = `false`
	)		const

◆ get_db() [2/5]

void ioda::ObsSpace::get_db	(	const std::string &	group,
		const std::string &	name,
		std::vector< float > &	vdata,
		const std::vector< int > &	chanSelect = `{ }`,
		bool	skipDerived = `false`
	)		const

◆ get_db() [3/5]

void ioda::ObsSpace::get_db	(	const std::string &	group,
		const std::string &	name,
		std::vector< int > &	vdata,
		const std::vector< int > &	chanSelect = `{ }`,
		bool	skipDerived = `false`
	)		const

transfer data from the obs container to vdata

The following get_db methods are the same except for the data type of the data being transferred (integer, float, double, string, DateTime). The caller needs to allocate the memory that the vdata parameter points to

Parameters

group	Name of container group (ObsValue, ObsError, MetaData, etc.)
name	Name of container variable
vdata	Vector where container data is being transferred to
chanSelect	Channel selection (list of channel numbers)
skipDerived	By default, this function will look for the variable `name` in the group `"Derived" + group` first and only if it doesn't exist will it look in the group `group`. Set this parameter to `true` to look only in the group `group`.

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◆ get_db() [4/5]

void ioda::ObsSpace::get_db	(	const std::string &	group,
		const std::string &	name,
		std::vector< std::string > &	vdata,
		const std::vector< int > &	chanSelect = `{ }`,
		bool	skipDerived = `false`
	)		const

◆ get_db() [5/5]

void ioda::ObsSpace::get_db	(	const std::string &	group,
		const std::string &	name,
		std::vector< util::DateTime > &	vdata,
		const std::vector< int > &	chanSelect = `{ }`,
		bool	skipDerived = `false`
	)		const

◆ get_dim_id()

ObsDimensionId ioda::ObsSpace::get_dim_id ( const std::string & dimName ) const

inline

return the standard dimension id for the given dimension name

Definition at line 203 of file src/ObsSpace.h.

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◆ get_dim_name()

std::string ioda::ObsSpace::get_dim_name ( const ObsDimensionId dimId ) const

inline

return the standard dimension name for the given dimension id

Definition at line 193 of file src/ObsSpace.h.

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◆ get_dim_size()

std::size_t ioda::ObsSpace::get_dim_size ( const ObsDimensionId dimId ) const

inline

return the standard dimension size for the given dimension id

Definition at line 198 of file src/ObsSpace.h.

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◆ getFillValue()

template<typename DataType >

DataType ioda::ObsSpace::getFillValue ( )

inlineprivate

get fill value for use in the obs_group_ object

Definition at line 491 of file src/ObsSpace.h.

◆ globalNumLocs()

std::size_t ioda::ObsSpace::globalNumLocs ( ) const

inline

return the total number of locations in the corresponding obs spaces across all MPI tasks

Definition at line 169 of file src/ObsSpace.h.

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◆ globalNumLocsOutsideTimeWindow()

std::size_t ioda::ObsSpace::globalNumLocsOutsideTimeWindow ( ) const

inline

return number of locations from obs source that were outside the time window

Definition at line 172 of file src/ObsSpace.h.

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◆ has()

bool ioda.ioda.ObsSpace::has	(	const std::string &	group,
		const std::string &	name,
		bool	skipDerived = `false`
	)		const

return true if variable name exists in group group or (unless skipDerived is set to true) "Derived" +group`.

This method checks for the existence of the group, name combination in the obs container. If the combination exists, "true" is returned, otherwise "false" is returned.

Definition at line 263 of file ObsSpace.cc.

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◆ index()

const std::vector<std::size_t>& ioda::ObsSpace::index ( ) const

inline

return reference to the index vector

This method returns a reference to the index vector data member. This is for read only access. The returned vector has length nlocs() and contains the original indices of locations from the input ioda file corresponding to locations stored in this ObsSpace object – i.e. those that were selected by the timing window filter and the MPI distribution.

Example 1: Suppose the RoundRobin distribution is used and and there are two MPI tasks (ranks 0 and 1). The even-numbered locations from the file will go to rank 0, and the odd-numbered locations will go to rank 1. This means that ObsSpace::index() will return the vector 0, 2, 4, 6, ... on rank 0 and 1, 3, 5, 7, ... on rank 1.

Example 2: Suppose MPI is not used and the file contains 10 locations in total, but locations 2, 3 and 7 are outside the DA timing window. In this case, ObsSpace::index() will return 0, 1, 4, 5, 6, 8, 9.

Definition at line 242 of file src/ObsSpace.h.

◆ initFromObsSource()

void ioda::ObsSpace::initFromObsSource ( ObsFrameRead & obsFrame )

private

initialize the in-memory obs_group_ (ObsGroup) object from the ObsIo source

Parameters

obsIo obs source object

Definition at line 579 of file ObsSpace.cc.

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◆ initial_obsvariables()

const oops::Variables& ioda::ObsSpace::initial_obsvariables ( ) const

inline

return the collection of simulated variables loaded from the input file

Definition at line 352 of file src/ObsSpace.h.

◆ loadVar() [1/2]

template<typename VarType >

void ioda::ObsSpace::loadVar	(	const std::string &	group,
		const std::string &	name,
		const std::vector< int > &	chanSelect,
		std::vector< VarType > &	varValues,
		bool	skipDerived
	)		const

Definition at line 699 of file ObsSpace.cc.

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◆ loadVar() [2/2]

template<typename VarType >

void ioda::ObsSpace::loadVar	(	const std::string &	group,
		const std::string &	name,
		const std::vector< int > &	chanSelect,
		std::vector< VarType > &	varValues,
		bool	skipDerived = `false`
	)		const

private

load a variable from the obs_group_ object

This function will load data from the obs_group_ object into the memory buffer (vector) varValues. The chanSelect parameter is only used when the variable is 2D radiance data (nlocs X nchans), and contains a list of channel numbers to be selected from the obs_group_ variable.

Parameters

group	Name of Group in obs_group_
name	Name of Variable in group
selectChan	Vector of channel numbers for selection
varValues	memory to load from obs_group_ variable
skipDerived	By default, this function will search for the variable `name` both in the group `group` and `"Derived" + group`. Set this parameter to `true` to search only in the group `group`.

◆ nchans()

size_t ioda::ObsSpace::nchans ( ) const

inline

return the number of channels in the container. If this is not a radiance obs type, then this will return zero.

Definition at line 181 of file src/ObsSpace.h.

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◆ nlocs()

size_t ioda::ObsSpace::nlocs ( ) const

inline

return the number of locations in the obs space. Note that nlocs may be smaller than global unique nlocs due to distribution of obs across multiple process elements.

Definition at line 177 of file src/ObsSpace.h.

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◆ nrecs()

std::size_t ioda::ObsSpace::nrecs ( ) const

inline

return the number of records in the obs space container

This is the number of sets of locations after applying the optional grouping.

Definition at line 186 of file src/ObsSpace.h.

◆ nvars()

std::size_t ioda::ObsSpace::nvars ( ) const

return the number of variables in the obs space container. "Variables" refers to the quantities that can be assimilated as opposed to meta data.

◆ obs_group_vars()

const std::vector< std::string > & ioda::ObsSpace::obs_group_vars ( ) const

return YAML configuration parameter: obsdatain.obsgrouping.group variables

Definition at line 243 of file ObsSpace.cc.

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◆ obs_sort_order()

std::string ioda::ObsSpace::obs_sort_order ( ) const

return YAML configuration parameter: obsdatain.obsgrouping.sort order

Definition at line 253 of file ObsSpace.cc.

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◆ obs_sort_var()

std::string ioda::ObsSpace::obs_sort_var ( ) const

return YAML configuration parameter: obsdatain.obsgrouping.sort variable

Definition at line 248 of file ObsSpace.cc.

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◆ obsAreSorted()

bool ioda::ObsSpace::obsAreSorted ( ) const

inline

true if the groups in the recidx data member are sorted

Definition at line 331 of file src/ObsSpace.h.

◆ obsname()

const std::string& ioda::ObsSpace::obsname ( ) const

inline

return the name of the obs type being stored

Definition at line 217 of file src/ObsSpace.h.

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◆ obsvariables()

const oops::Variables& ioda::ObsSpace::obsvariables ( ) const

inline

return the collection of all simulated variables

Definition at line 349 of file src/ObsSpace.h.

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◆ openCreateVar()

template<typename VarType >

Variable ioda::ObsSpace::openCreateVar	(	const std::string &	varName,
		const std::vector< std::string > &	varDimList
	)

inlineprivate

open an obs_group_ variable, create the varialbe if necessary

Definition at line 551 of file src/ObsSpace.h.

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◆ operator=()

ObsSpace& ioda::ObsSpace::operator= ( const ObsSpace & )

privatedelete

disable the "=" operator

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◆ params()

const ObsSpaceParameters& ioda::ObsSpace::params ( ) const

inline

This method will return the associated parameters

Definition at line 152 of file src/ObsSpace.h.

◆ print()

void ioda.ioda.ObsSpace::print ( std::ostream & os ) const

private

print function for oops::Printable class

Parameters

os	output stream

This method provides a way to print an ObsSpace object in an output stream.

Definition at line 436 of file ObsSpace.cc.

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◆ put_db() [1/5]

void ioda::ObsSpace::put_db	(	const std::string &	group,
		const std::string &	name,
		const std::vector< double > &	vdata,
		const std::vector< std::string > &	dimList = `{ "nlocs" }`
	)

◆ put_db() [2/5]

void ioda::ObsSpace::put_db	(	const std::string &	group,
		const std::string &	name,
		const std::vector< float > &	vdata,
		const std::vector< std::string > &	dimList = `{ "nlocs" }`
	)

◆ put_db() [3/5]

void ioda::ObsSpace::put_db	(	const std::string &	group,
		const std::string &	name,
		const std::vector< int > &	vdata,
		const std::vector< std::string > &	dimList = `{ "nlocs" }`
	)

transfer data from vdata to the obs container

The following put_db methods are the same except for the data type of the data being transferred (integer, float, double, string, DateTime). The caller needs to allocate and assign the memory that the vdata parameter points to.

Parameters

group	Name of container group (ObsValue, ObsError, MetaData, etc.)
name	Name of container variable
vdata	Vector where container data is being transferred from
dimList	Vector of dimension names (for creating variable if needed)

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◆ put_db() [4/5]

void ioda::ObsSpace::put_db	(	const std::string &	group,
		const std::string &	name,
		const std::vector< std::string > &	vdata,
		const std::vector< std::string > &	dimList = `{ "nlocs" }`
	)

◆ put_db() [5/5]

void ioda::ObsSpace::put_db	(	const std::string &	group,
		const std::string &	name,
		const std::vector< util::DateTime > &	vdata,
		const std::vector< std::string > &	dimList = `{ "nlocs" }`
	)

◆ readObsSource() [1/3]

template<>

bool ioda::ObsSpace::readObsSource	(	ObsFrameRead &	obsFrame,
		const std::string &	varName,
		std::vector< std::string > &	varValues
	)

Definition at line 556 of file ObsSpace.cc.

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◆ readObsSource() [2/3]

template<typename VarType >

bool ioda::ObsSpace::readObsSource	(	ObsFrameRead &	obsFrame,
		const std::string &	varName,
		std::vector< VarType > &	varValues
	)

Definition at line 532 of file ObsSpace.cc.

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◆ readObsSource() [3/3]

template<typename VarType >

bool ioda::ObsSpace::readObsSource	(	ObsFrameRead &	obsFrame,
		const std::string &	varName,
		std::vector< VarType > &	varValues
	)

private

read in values for variable from obs source

Parameters

obsFrame	obs frame object
varName	Name of variable in obs source object
varValues	values for variable

◆ recidx_all_recnums()

std::vector< std::size_t > ioda::ObsSpace::recidx_all_recnums ( ) const

return all record numbers from the recidx_ data member

Definition at line 421 of file ObsSpace.cc.

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◆ recidx_begin()

const ObsSpace::RecIdxIter ioda::ObsSpace::recidx_begin ( ) const

Return the begin iterator associated with the recidx_ data member.

Definition at line 383 of file ObsSpace.cc.

◆ recidx_end()

const ObsSpace::RecIdxIter ioda::ObsSpace::recidx_end ( ) const

Return the end iterator associated with the recidx_ data member.

Definition at line 388 of file ObsSpace.cc.

◆ recidx_has()

bool ioda::ObsSpace::recidx_has ( const std::size_t recNum ) const

true if given record number exists in the recidx_ data member

Parameters

recNum Record number being searched for

Definition at line 393 of file ObsSpace.cc.

◆ recidx_recnum()

std::size_t ioda::ObsSpace::recidx_recnum ( const RecIdxIter & irec ) const

return record number pointed to by the given iterator

Parameters

irec	Iterator into the recidx_ data member

Definition at line 399 of file ObsSpace.cc.

◆ recidx_vector() [1/2]

const std::vector< std::size_t > & ioda::ObsSpace::recidx_vector ( const RecIdxIter & irec ) const

return record number vector pointed to by the given iterator

Parameters

irec	Iterator into the recidx_ data member

Definition at line 404 of file ObsSpace.cc.

◆ recidx_vector() [2/2]

const std::vector< std::size_t > & ioda::ObsSpace::recidx_vector ( const std::size_t recNum ) const

return record number vector selected by the given record number

Parameters

recNum Record number being searched for

Definition at line 409 of file ObsSpace.cc.

◆ recnum()

const std::vector<std::size_t>& ioda::ObsSpace::recnum ( ) const

inline

return reference to the record number vector

Definition at line 223 of file src/ObsSpace.h.

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◆ resizeNlocs()

void ioda::ObsSpace::resizeNlocs	(	const Dimensions_t	nlocsSize,
		const bool	append
	)

private

resize along nlocs dimension

Parameters

nlocsSize	new size to either append or reset
append	when true append nlocsSize to current size, otherwise reset size

Definition at line 684 of file ObsSpace.cc.

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◆ save()

void ioda.ioda.ObsSpace::save ( )

save the obs space data into a file (if obsdataout specified)

This function will save the obs space data into a file, but only if the obsdataout parameter is specified in the YAML configuration. Note that this function will do nothing if the obsdataout specification is not present.

The purpose of this save function is to fix an issue where the hdf5 library closes the file (via a C API) during the time when the ObsSpace destructor (C++) is still writing to that file. These actions can sometimes get out of sync since they are being triggered from different sources during the clean up after a job completes.

Definition at line 204 of file ObsSpace.cc.

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◆ saveToFile()

void ioda::ObsSpace::saveToFile ( )

private

Dump the database into the output file.

Definition at line 1066 of file ObsSpace.cc.

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◆ saveVar() [1/2]

template<typename VarType >

void ioda::ObsSpace::saveVar	(	const std::string &	group,
		std::string	name,
		const std::vector< VarType > &	varValues,
		const std::vector< std::string > &	dimList
	)

Definition at line 753 of file ObsSpace.cc.

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◆ saveVar() [2/2]

template<typename VarType >

void ioda::ObsSpace::saveVar	(	const std::string &	group,
		std::string	name,
		const std::vector< VarType > &	varValues,
		const std::vector< std::string > &	dimList
	)

private

save a variable to the obs_group_ object

Parameters

group	Name of Group in obs_group_
name	Name of Variable in group.
varValues	values to be saved
dimList	Vector of dimension names (for creating variable if needed)

If the group group does not contain a variable with the specified name, but this name has the form <string>_<integer> and obs_group_ contains an nchans dimension, this function will save varValues in the slice of variable <string> corresponding to channel <integer>. If channel <integer> does not exist or the variable <string> already exists but is not associated with the nchans dimension, an exception will be thrown.

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◆ splitChanSuffix()

void ioda::ObsSpace::splitChanSuffix	(	const std::string &	group,
		const std::string &	name,
		const std::vector< int > &	chanSelect,
		std::string &	nameToUse,
		std::vector< int > &	chanSelectToUse,
		bool	skipDerived = `false`
	)		const

private

split off the channel number suffix from a given variable name

If the given variable name does not exist, the channelSelect vector is empty, and the given variable name has a suffix matching "_[0-9][0-9]*" (ie, a numeric suffix), then this routine will strip off the channel number from the name and place that channel number into the ouput canSelectToUse vector. The new name will be returned in the nameToUse string. This is being done for backward compatibility until the ufo Variables class and its clients are modified to handle a single variable name and a vector of channel numbers.

Parameters

group	Name of Group in obs_group_
name	Name of Variable in group
selectChan	Vector of channel numbers for selection
varName	Name of Variable after splitting off the channel number
skipDerived	By default, this function will search for the variable `name` both in the group `group` and `"Derived" + group`. Set this parameter to `true` to search only in the group `group`.

Definition at line 991 of file ObsSpace.cc.

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◆ storeVar() [1/2]

template<typename VarType >

void ioda::ObsSpace::storeVar	(	const std::string &	varName,
		std::vector< VarType > &	varValues,
		const Dimensions_t	frameStart,
		const Dimensions_t	frameCount
	)

Definition at line 882 of file ObsSpace.cc.

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◆ storeVar() [2/2]

template<typename VarType >

void ioda::ObsSpace::storeVar	(	const std::string &	varName,
		std::vector< VarType > &	varValues,
		const Dimensions_t	frameStart,
		const Dimensions_t	frameCount
	)

private

store a variable in the obs_group_ object

Parameters

obsIo	obs source object
varName	Name of obs_group_ variable for obs_group_ object
varValues	Values for obs_group_ variable
frameStart	is the start of the ObsFrame
frameCount	is the size of the ObsFrame

◆ windowEnd()

const util::DateTime& ioda::ObsSpace::windowEnd ( ) const

inline

This method will return the end of the DA timing window

Definition at line 146 of file src/ObsSpace.h.

◆ windowStart()

const util::DateTime& ioda::ObsSpace::windowStart ( ) const

inline

This method will return the start of the DA timing window

Definition at line 143 of file src/ObsSpace.h.

Member Data Documentation

◆ chan_num_to_index_

std::map<int, int> ioda::ObsSpace::chan_num_to_index_

private

map to go from channel number (not necessarily consecutive) to channel index (consecutive, starting from zero).

Definition at line 388 of file src/ObsSpace.h.

◆ commMPI_

const eckit::mpi::Comm& ioda::ObsSpace::commMPI_

private

MPI communicator.

Definition at line 372 of file src/ObsSpace.h.

◆ dim_info_

ObsDimInfo ioda::ObsSpace::dim_info_

private

dimension information for variables in this obs space

Definition at line 384 of file src/ObsSpace.h.

◆ dims_attached_to_vars_

VarDimMap ioda::ObsSpace::dims_attached_to_vars_

private

map showing association of dim names with each variable name

Definition at line 418 of file src/ObsSpace.h.

◆ dist_

std::shared_ptr<const Distribution> ioda::ObsSpace::dist_

private

MPI distribution object.

Definition at line 403 of file src/ObsSpace.h.

◆ gnlocs_

std::size_t ioda::ObsSpace::gnlocs_

private

total number of locations

Definition at line 375 of file src/ObsSpace.h.

◆ gnlocs_outside_timewindow_

std::size_t ioda::ObsSpace::gnlocs_outside_timewindow_

private

number of nlocs from the obs source that are outside the time window

Definition at line 378 of file src/ObsSpace.h.

◆ indx_

std::vector<std::size_t> ioda::ObsSpace::indx_

private

indexes of locations to extract from the input obs file

Definition at line 406 of file src/ObsSpace.h.

◆ known_be_selections_

std::map<std::vector<std::string>, Selection> ioda::ObsSpace::known_be_selections_

private

cache for backend selection

Definition at line 424 of file src/ObsSpace.h.

◆ known_fe_selections_

std::map<std::vector<std::string>, Selection> ioda::ObsSpace::known_fe_selections_

private

cache for frontend selection

Definition at line 421 of file src/ObsSpace.h.

◆ nrecs_

std::size_t ioda::ObsSpace::nrecs_

private

number of records

Definition at line 381 of file src/ObsSpace.h.

◆ obs_group_

ObsGroup ioda::ObsSpace::obs_group_

private

observation data store

Definition at line 391 of file src/ObsSpace.h.

◆ obs_params_

ObsSpaceParameters ioda::ObsSpace::obs_params_

private

obs io parameters

Definition at line 394 of file src/ObsSpace.h.

◆ obsname_

std::string ioda::ObsSpace::obsname_

private

name of obs space

Definition at line 397 of file src/ObsSpace.h.

◆ obsvars_

oops::Variables ioda::ObsSpace::obsvars_

private

Observation "variables" to be simulated.

Definition at line 400 of file src/ObsSpace.h.

◆ recidx_

RecIdxMap ioda::ObsSpace::recidx_

private

profile ordering

Definition at line 412 of file src/ObsSpace.h.

◆ recidx_is_sorted_

bool ioda::ObsSpace::recidx_is_sorted_

private

indicator whether the data in recidx_ is sorted

Definition at line 415 of file src/ObsSpace.h.

◆ recnums_

std::vector<std::size_t> ioda::ObsSpace::recnums_

private

record numbers associated with the location indexes

Definition at line 409 of file src/ObsSpace.h.

◆ winbgn_

const util::DateTime ioda::ObsSpace::winbgn_

private

Beginning of DA timing window.

Definition at line 366 of file src/ObsSpace.h.

◆ winend_

const util::DateTime ioda::ObsSpace::winend_

private

End of DA timing window.

Definition at line 369 of file src/ObsSpace.h.

The documentation for this class was generated from the following files:

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Parameters_

◆ RecIdxIter

◆ RecIdxMap

Constructor & Destructor Documentation

◆ ObsSpace() [1/2]

◆ ObsSpace() [2/2]

◆ ~ObsSpace()

Member Function Documentation

◆ buildRecIdxUnsorted()

◆ buildSortedObsGroups()

◆ comm()

◆ createChannelSelections()

◆ createMissingObsErrors()

◆ createObsGroupFromObsFrame()

◆ createVariables()

◆ derived_obsvariables()

◆ distname()

◆ distribution()

◆ dtype()

◆ extendObsSpace()

◆ extendVariable() [1/2]

◆ extendVariable() [2/2]

◆ fillChanNumToIndexMap()

◆ get_db() [1/5]

◆ get_db() [2/5]

◆ get_db() [3/5]

◆ get_db() [4/5]

◆ get_db() [5/5]

◆ get_dim_id()

◆ get_dim_name()

◆ get_dim_size()

◆ getFillValue()

◆ globalNumLocs()

◆ globalNumLocsOutsideTimeWindow()

◆ has()

◆ index()

◆ initFromObsSource()

◆ initial_obsvariables()

◆ loadVar() [1/2]

◆ loadVar() [2/2]

◆ nchans()

◆ nlocs()

◆ nrecs()

◆ nvars()

◆ obs_group_vars()

◆ obs_sort_order()

◆ obs_sort_var()

◆ obsAreSorted()

◆ obsname()

◆ obsvariables()

◆ openCreateVar()

◆ operator=()

◆ params()

◆ print()

◆ put_db() [1/5]

◆ put_db() [2/5]

◆ put_db() [3/5]

◆ put_db() [4/5]

◆ put_db() [5/5]

◆ readObsSource() [1/3]

◆ readObsSource() [2/3]

◆ readObsSource() [3/3]

◆ recidx_all_recnums()

◆ recidx_begin()

◆ recidx_end()

◆ recidx_has()

◆ recidx_recnum()

◆ recidx_vector() [1/2]

◆ recidx_vector() [2/2]

◆ recnum()

◆ resizeNlocs()

◆ save()

◆ saveToFile()

◆ saveVar() [1/2]